Variant report

Variant	rs12880781
Chromosome Location	chr14:65576257-65576258
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:65567727..65571769-chr14:65574635..65579781,8	MCF-7	breast:
2	chr14:65574956..65578020-chr14:65578405..65580427,3	MCF-7	breast:
3	chr14:65569605..65571519-chr14:65575666..65579395,3	MCF-7	breast:
4	chr14:65571192..65573054-chr14:65576225..65578951,2	K562	blood:

Variant related genes	Relation type
ENSG00000125952	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10151162	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs10873180	0.82[EUR][1000 genomes]
rs10873181	0.81[EUR][1000 genomes]
rs10873182	0.81[EUR][1000 genomes]
rs11158572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158573	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158574	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158578	0.81[EUR][1000 genomes]
rs1124751	0.84[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs1124752	0.84[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs11625045	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11626156	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11626496	0.90[ASN][1000 genomes]
rs11627382	0.84[MEX][hapmap]
rs11627859	0.90[ASN][1000 genomes]
rs12147959	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1256417	0.82[EUR][1000 genomes]
rs1270074	0.83[CEU][hapmap]
rs1271582	0.84[CEU][hapmap]
rs12884836	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12887607	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12888794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12893404	0.80[ASN][1000 genomes]
rs17825846	0.91[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1953228	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1953232	0.84[CEU][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs1957948	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1998688	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2093989	0.87[EUR][1000 genomes]
rs2763888	0.86[EUR][1000 genomes]
rs2781373	0.84[CEU][hapmap];0.80[TSI][hapmap];0.84[EUR][1000 genomes]
rs2781374	0.85[EUR][1000 genomes]
rs2898863	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34062462	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35002541	0.94[ASN][1000 genomes]
rs35176994	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35769504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3783720	0.82[MEX][hapmap]
rs45604339	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4899160	0.84[MEX][hapmap]
rs4899161	0.92[CEU][hapmap];0.84[CHB][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs4902358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4902360	0.84[CEU][hapmap]
rs4902361	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs4902364	0.90[ASN][1000 genomes]
rs4902365	0.90[ASN][1000 genomes]
rs4902367	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55658675	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61987428	0.81[EUR][1000 genomes]
rs61987429	0.81[EUR][1000 genomes]
rs7143495	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7144259	0.91[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7154852	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7156617	0.92[CEU][hapmap];0.84[CHB][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs7159443	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs7160037	0.84[MEX][hapmap]
rs7161394	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs762810	0.87[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[YRI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8004805	0.83[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8009396	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8009714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010213	0.82[EUR][1000 genomes]
rs8015330	0.88[ASN][1000 genomes]
rs8181937	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8181938	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8181939	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs868814	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs884683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs942626	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs942627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs942628	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832816	chr14:65473244-65644645	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12880781	RAB15	cis	lymphoblastoid	seeQTL
rs12880781	MAX	cis	parietal	SCAN
rs12880781	WDR89	cis	cerebellum	SCAN
rs12880781	MAX	cis	cerebellum	SCAN
rs12880781	CHURC1	cis	parietal	SCAN
rs12880781	GPX2	cis	cerebellum	SCAN
rs12880781	SIX4	cis	cerebellum	SCAN
rs12880781	RAB15	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65575600-65577600	Enhancers	K562	blood
2	chr14:65576000-65576400	Enhancers	Fetal Thymus	thymus

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